The problem with Vancian magic is that the player only has to rest to refill their slots, thereby trivializing management of spells. Just spam the spells from their slots, faceroll every encounter, then rest. Rinse Repeat.
There isn't much wrong with Vancian magic providing that resting is strictly restricted. The IE games utterly failed at this, and only with the Tactics mod (later, SCS2) did we start to see a concerted implementation, albeit only in BG2's starter dungeon (where resting was only permitted once, to fill your spell slots). After which resting caused 100% respawns of resource-draining enemies. The more you rested, the less you had, until you had nothing and had to reload. Apart from that, the risk of being waylaid was mostly trivial: the number, the type, the frequency - all were a joke. This goes for every IE game, wherein respawns from resting are even welcome - more experience!
Temple of Elemental Evil used a respawning approach that was similar, but it was the high % chance of a respawn on resting that would dissuade you, and the fact that even a rat trashmob is going to take time to defeat under a superior turn-based system. You realized that you should probably find a safe-haven, or teleport (the arcane spell) out of the Temple to rest. Specific user-made modules for NWN1 handled resting with a welcome heavy hand, it was restricted to once every four hours which is 8 mins real-time. This stops rest abuse except for people who are happy to leave their PC while they do something else.
Moving on... the argument that after a certain point Origins mages become OP doesn't really put cooldowns in a negative light, because after a certain point - and much earlier than Origins - mages in the IE decimate everything with a vast array of direct dmg, buffing, disablers and phantasms. The argument that Storm of the Century is an awesome "I WIN" button can be applied to several IE spells I can name off the top of my head. In Baldur's Gate, the three-pronged Sleep + Blindness + Web dominates all. The most effective spells at higher levels are simply amped-upped versions of these. In BG2, the level 2 Web spell remains dominant - but now you have mages who can stack down 10 each using sequencers - and it's common knowledge that there's too much other OP to bother listing.
Origins balances cooldowns by throwing more enemies at you in sustained encounters, which require constant adjustment and re-evaluation. On Nightmare difficulty (which all IE vets should play, right off the bat), Origins throws more enemies at you, buffs them in myriad ways, and increases their AI (lieutenants will favor their more powerful abilities, more often). In contrast BG has for the most part trivial trashmobs, of which one placement of Sleep or Web is enough to win. And when you scale difficulty up, you merely take more dmg and inflict less.
Lastly, the charges against Origins encounters not having something inbetween boss and trashmob aren't really true. There are many tougher encounters, in which a party's resources might be stretched. And while I can faceroll everything on Nightmare, that's only because I know the spells to take and when to use them. Which is why I can faceroll BG2 with even less effort with a solo sorcerer, just like everyone else.
Cooldowns or Vancian, it doesn't really matter providing there are restrictions that balance out the nature of both systems.